I am reading about mono-alphabetic ciphers, which are prone to letter frequency analysis. To counter this, we can provide multiple substitutions, known has homophones for a single letter e.g. e could be assigned 17, 74, 35, 21. Each homophone could be assigned in rotation or randomly.
This is where I am confused:
Even with homophones, each element of plaintext affects only one element of ciphertext, and multiple-letter patterns (e.g. diagram frequencies) still survive in the ciphertext, making cryptanalysis relatively straight forward.
How do multiple-letter patterns survive? For example if for h we have homophones 17, 74, 35, 21 and for t we have 11, 69, 27, 24, th could be 11 17 or 11 74 or 11 35 or 69 21 etc.